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39 results for “oilseed rape”
Weed surveys in Oilseed rape fields in the LTSER Zone Atelier Plaine & Val de Sèvre
<p>Dataset used in Berquer, A.; Martin, O.; Gaba, S. Landscape Is the Main Driver of Weed Assemblages in Field Margins but Is Outperformed by Crop Competition in Field Cores. Plants 2021, 10, 2131. https://doi.org/10.3390/plants10102131</p> <p>Because there personnal and sensitive data, agricultural practices data are not given. Please contact Sabrina Gaba or Vincent Bretagnolle if you are interested in a collaborative project.</p>
Pathogen lifestyle determines host genetic signature of quantitative disease resistance loci in oilseed rape (Brassica napus)
<p>Supplemental datasets associated with publication: Pathogen lifestyle determines host genetic signature of quantitative disease resistance loci in oilseed rape (<em>Brassica napus</em>)</p> <p><strong>Abstract</strong></p> <ul> <li>Crops are affected by several pathogens, but these are rarely studied in parallel to identify common and unique genetic factors controlling diseases. Broad-spectrum quantitative disease resistance (QDR) is desirable for crop breeding as it confers resistance to several pathogen species.</li> <li>Here, we use associative transcriptomics (AT) to identify candidate gene loci associated with <em>Brassica napus</em> constitutive QDR to four contrasting fungal pathogens: <em>Alternaria brassicicola</em>, <em>Botrytis cinerea</em>, <em>Pyrenopeziza</em><em> brassicae</em> and <em>Verticillium longisporum. </em>We did not identify any loci associated with broad-spectrum QDR to fungal pathogens with contrasting lifestyles. Instead, we observed QDR dependent on the lifestyle of the pathogen—hemibiotrophic and necrotrophic pathogens had distinct QDR responses and associated loci, including some loci associated with early immunity. Furthermore, we identify a genomic deletion associated with resistance to <em>V. longisporum </em>and potentially broad-spectrum QDR.</li> <li>This is the first time AT has been used for several pathosystems simultaneously to identify host genetic loci involved in broad-spectrum QDR. We highlight constitutively expressed candidate loci for broad-spectrum QDR with no antagonistic effects on susceptibility to the other pathogens studies as candidates for crop breeding. In conclusion, this study represents and advancement in our understanding if broad-spectrum QDR in <em>B. napus </em>and is a significant resource for the scientific community. </li> </ul> <p><strong>Description of data files</strong></p> <p><strong>Full dataset for input into AT analysis </strong>Full datasets (infection phenotypes for <em>A. brassicicola, B. cinerea, </em>or <em>V.longisporum, </em>ROS measurements for chitin, flg22, or elf18) and link to original <em>P. brassicae </em>dataset. These datasets were used for input into the Associative Transcriptomics pipeline (Nichols, 2022, <a href="https://github.com/bsnichols/GAGA. https://zenodo.org/badge/latestdoi/512807075">https://github.com/bsnichols/GAGA. https://zenodo.org/badge/latestdoi/512807075</a>). </p> <p><strong>Table S1 </strong>Mean, normalized phenotype data for resistance to pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae </em>and <em>Verticillium longisporum</em>) and ROS response induced by PAMPS (chitin, flg22, and elf18). These data were used for association transcriptomic analysis.<strong> </strong></p> <p><strong>Table S2 </strong>Full list of single nucleotide polymorphism (SNP) markers and significance levels from genome-wide association (GWA) analyses for resistance to pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae </em>and <em>Verticillium longisporum</em>) and ROS response induced by PAMPS (chitin, flg22, and elf18). Each excel tab contains the analyses for a single trait. The best fit model for GWA analysis is indicated in the tab title. Manhattan plots showing marker-trait association are included for data visualization; x-axis indicates SNP location along the chromosome; the y-axis indicates the -log10(p) (P value). Qqplots are included to demonstrate model fit.</p> <p><strong>Table S3</strong> Full list of gene expression markers (GEMs) and significance levels from GEM analyses for resistance to pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae and Verticillium longisporum</em>) and ROS response induced by PAMPS (chitin, flg22, and elf18). Each excel tab contains the analyses for a single trait. Manhattan plots showing marker-trait association are included for data visualization; x-axis indicates GEM location along the chromosome; the y-axis indicates the -log10(p) (P value). </p> <p><strong>Table S4 </strong>184 gene expression markers (GEMs) associated with chitin-induced ROS compared with GEMs associated with resistance to pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae </em>and<em> Verticillium longisporum</em>) and ROS response induced by flg22, and elf18. Lists correspond to Venn diagrams in Fig. 2. The first tab includes all 184 GEMs associated with chitin-induced ROS. The subsequent tabs include lists of shared GEMs associated with chitin-induced ROS response and each additional trait (quantitative disease resistance (QDR) to each fungal pathogen or additional PAMP-induced ROS responses). The title of each tab indicates the data included in each comparison and the number of shared GEMs. Predicted <em>Arabidopsis thaliana</em> orthologs and corresponding descriptions are shown where possible. </p> <p><strong>Table S5</strong> Enrichment analyses to determine if the number of gene expression markers (GEMs) shared between different lists is greater than the number of GEMs that would be expected by chance (e.g., lists of quantitative disease resistance (QDR) GEMs for two fungal pathogens). The representation factor is the number of overlapping GEMs divided by the expected number of overlapping GEMs drawn from two independent groups (traits), considering the total number of GEMs sequenced (53884). A representation factor > 1 indicates more overlap than expected of two groups, a representation factor < 1 indicates less overlap than expected, and a representation factor of 1 indicates that the two groups by the number of genes expected for independent groups of genes. </p> <p><strong>Table S6 R</strong>esults from Weighted Co-expression Gene Network Analysis (WGCNA). The first tab indicates significant modules from WGCNA analysis. Black and magenta modules are associated with antagonistic effects on resistance/susceptibility to all four pathogens. The second tab includes a full list of the GEM markers (Table S3), which are in significant WGCNA modules. The third, fourth and, fifth tabs indicate all significant GEMs in the black module, GO terms associated with GEMs in the black module, and all GO terms associated with the black module, respectively. The sixth, seventh and, eighth tabs indicate all significant GEMs in the magenta module, GO terms associated with GEMs in the magenta module, and all GO terms associated with the magenta module, respectively.</p> <p><strong>Table S7 </strong>Shared gene expression markers (GEMs) associated with resistance to different pathogens (<em>Alternaria brassicicola, Botrytis cinerea, Pyrenopeziza brassicae </em>and <em>Verticillium longisporum</em>). Lists correspond to matrices and Venn diagrams in Fig. 3. The first tab includes all GEMs associated quantitative disease resistance (QDR) to the fungal pathogens. The subsequent tabs include lists of shared GEMs associated with QDR to two or more fungal pathogens. The title of each tab indicates the data included in each comparison and the number of shared GEMs. Predicted <em>Arabidopsis thaliana</em> orthologs and corresponding descriptions are shown where possible. </p> <p><strong>Table S8 </strong>List of genes in linkage disequilibrium with the top marker for <em>Verticillium longisporum</em> resistance from genome-wide association (GWA) analysis on chromosome A09 (107 genes)(Tab 1) and the homoeologous region on C08 (Tab 2). Their percentage identity and query coverage in <em>Brassica napus</em> reference genotypes Quinta, Tapidor, Westar and Zhongshuang 11 compared to the <em>B. napus</em> pantranscriptome is indicated. Predicted <em>Arabidopsis thaliana</em> orthologs and corresponding descriptions are shown where possible. </p> <p> </p>
Farmers' fields network of oilseed rape intercropped with service plant in Western Switzerland.
<p>These data are associated with the publication of Bousselin et al. (2024) in which the experiment and the protocols are explained into details.</p> <p><span>Bousselin, X., Lorin, M., Valantin-Morison, M. </span><em>et al.</em><span> Determinants of oilseed rape-service plant intercropping performance variability across a farmers’ fields network in Western Switzerland. </span><em>Agron. Sustain. Dev.</em><span> </span><strong>44</strong><span>, 40 (2024). https://doi.org/10.1007/s13593-024-00972-6</span></p>
Chromosome-scale assembly of winter oilseed rape Brassica napus
<p>The files correspond to data and results referenced in research article titled "Chromosome-scale assembly of winter oilseed rape Brassica napus".</p> <p>Data files below were used in the scaffolding process of genome assembly:</p> <ol> <li>Genetic maps (csv) <ul> <li>ExR53-DH_60kSNPmap</li> <li>ExV8-DH_60kSNPmap</li> </ul> </li> </ol> <p>Result files below are assembled sequences of the genome and the predicted annotation:</p> <ol> <li>Genome assembly (Express617_v1.fa.gz)</li> <li>Predicted coding sequences (Express617_v1_cds.fa.gz)</li> <li>Predicted coding sequences (Express617_v1_gene.gff3.gz)</li> <li>Predicted protein sequences (Express617_v1_protein.fa.gz)</li> <li>Predicted repetitive elements (Express617_v1_repeats.gff.gz)</li> </ol>
Oilseed rape plant phytometers in an agricultural landscape in France - LTSER Zone Atelier Plaine & Val de Sèvre
<p>Fruit set as a proxy of pollination efficiency measured using oilseed rape plant phytometers placed in grasslands, cereals and oilseed rape fields in the LTSER Zone Atelier Plaine & Val de Sèvre. The individual contributions of different processes to pollination were determined using a bagging experiment (large-, small- and osmolux) on plant phytometers.</p> <p>Landscape metrics are available upon reasonable request</p>
Biomass estimation of oilseed rape using the light use efficiency model in Bavaria (Atlas) in LandKlif project
<p>This dataset shows the predicted biomass (g/m2) of oilseed rape (OSR) using the light use efficiency (LUE) model for Bavaria in 2019. The LUE model uses satellite data (Landsat-8, MODIS) and climate data (temperature and solar radiation) to calculate the plant biomass. The crop yield is predicted and validated at district level using LfStat data. The validation results show an R2 of 0.79 with an RMSE of 2.21 dt/ha. </p> <p>This dataset is conducted under LandKlif project. LandKlif is funded by the <a href="https://www.stmwk.bayern.de/englisch.html"><strong>Bavarian State Ministry of Science and the Arts</strong></a> within the <a href="https://www.bayklif.de/"><strong>Bavarian Climate Research Network (bayklif)</strong></a><strong>. </strong> Within the five year funding period of bayklif, five interdisciplinary senior research associations and five junior research groups are be financed with a total sum of 18 million Euro. <strong>LandKliF</strong>, as one of the five interdisciplinary senior research associations, addresses the effects of climate change on biodiversity and ecosystem services in semi-natural, agricultural and urban landscapes.</p>
Fig.2. The phylogenetic tree for 72 in Genetic Diversity Of (Brassica Napus L.) Spring Oilseed Rape
Fig.2. The phylogenetic tree for 72 individual of Brassica napus constructed on the basis of RAPD data: M - 'Maskot, S - 'Sw Savan', H -'Heros', U -'Ural', L -'Landmark'
Fig.1 in Genetic Diversity Of (Brassica Napus L.) Spring Oilseed Rape
Fig.1. DNA fingerprints from different samples of different oilseed rape cultivars obtained by PCR with primers: OPA-01-S1-S6-'SwSavan'; OPA-04-H1-H6-'Heros'; OPA-04-U1-U6-'Ural'; OPA-09-L1- L5-'Landmark'; OPA11-M1-M6-'Maskot'. M-Gene RulerTM 100 bp DNA Ladder Plus (MBI Fermentas)
Fig.1 in Commonly Found Species Of Ceutorhynchus (Coleoptera: Curculionidae) On The Oilseed Rape In Latvia
Fig.1. The number of C. pallidactylus (imago) and invasion level (%) in Zemgales area Major activity of C. obstrictus was observed during the flowering stage of oilseed rape (BBCH 60- 70), when the trapped insects constituted 32% of all weevils.
Data from: Earlier flowering of winter oilseed rape compensates for higher pest pressure in warmer climates
<p>Pest abundance and timing of migration relative to the vulnerable crop stage influence the severity of crop damage and yield loss to insect pests in oilseed rape (OSR). Both abundance and timing are influenced by landscape composition, changes therein due to crop rotation, and temperature. The need for sustainable and temperature-adapted management strategies of OSR pests due to the environmental harm of current conventional practices and global warming calls for a better understanding of the combined effects of landscape composition and temperature on pest abundances, larval parasitism, crop damage and yield, but also of the role of crop phenology for crop damage and yield under field conditions. Here, 29 winter OSR crops were studied along a multi-annual mean temperature gradient (MAT, 1981–2010) in Bavaria, Germany. We measured pest abundances (pollen beetles, stem weevils), crop damage (bud loss, stem tunnelling), pollen beetle larval parasitism and crop yield and calculated Julian dates of flowering from biweekly observations of growth stages. Pest abundances and parasitism were analysed with regard to MAT and landscape parameters at six scales (non-crop habitat and OSR area, change in the proportion of OSR area relative to the previous year; 0.6 km, and 1–5 km in 1-km steps), while analysis of crop damage and yield also included Julian date of flowering. Pollen beetle abundance was increased under higher MAT, but less strongly when OSR proportions were high (1-km scale) and not strongly reduced relative to the previous year (5-km scale), while pollen beetle larval parasitism was overall low but exceeded 30% (considered as threshold for effective natural control) occasionally under both low and high MAT. In contrast to abundance of adult pollen beetles, stem weevil larval abundance – as well as stem damage – did not respond to landscape composition nor MAT. Despite high abundance of adult pollen beetles under high MAT, crop yield was high (and the proportion of bud loss low) under high MAT when OSR flowered early. Our results underpin the potential of targeted landscape management (e.g. through regionally coordinated crop rotations) and timing of flowering (e.g. through cultivar choice) for environment-friendly and temperature-adapted pest management in winter OSR.</p>
Data from: Earlier flowering of winter oilseed rape compensates for higher pest pressure in warmer climates
Open the record for dataset details and reuse information.
Diversity of parasitoid wasps (Insecta, Hymenoptera) in oilseed rape fields in Serbia
<p>Oilseed rape is an important crop grown worldwide and used for various purposes, including oil extraction and animal feed. In Europe, there are six major pest species and several other minor pests that can significantly affect oilseed rape production, requiring growers to effectively control them in order to ensure crop yield. The host-parasitoid complexes of these pests have been studied in detail and recorded mainly in western, central and northern Europe. As an abundant source of pollen and nectar, oilseed rape may also be attractive to other parasitoids that do not have direct trophic interactions with oilseed rape pest species. The aim of this study is to fill the knowledge gap regarding the wider parasitoid community in oilseed rape fields, particularly in southern Europe.</p> <p>During the two-year study, a total of 3135 specimens of primary and secondary parasitoids were sampled, of which 2855 were found in oilseed rape fields and 280 in semi-natural habitats. We found 153 taxa, of which 119 were found in oilseed rape fields and 87 in semi-natural habitats. We identified 31 genera (33 species) as parasitoids of oilseed rape pests, 54 genera (97 species) parasitising non-pest species and 10 genera (23 species) as possible parasitoids of oilseed rape pests. This study shows that the parasitoid community in oilseed rape fields is very diverse and that includes parasitoids of both oilseed rape pest and non-pest species.</p>
Algal growth, bumblebee colony and individual development, bee behavior and yield of oilseed rape under a trophic cascade and extreme weather
<p><span>Trophic cascades in the aquatic environment constitute important mechanisms for improving water quality. However, how the presence or non-presence of these trophic cascades may affect interactions across the aquatic-terrestrial interface remains poorly investigated. Pollinators such as bees may be especially vulnerable to changes in water resource quality induced by trophic cascades. Understanding how aquatic trophic cascades affect bees and pollination becomes even more pressing under ongoing climate change due to increased physiological demands for water under extreme weather events.</span><span>In a novel field experiment combining terrestrial and aquatic mesocosms, we aimed to test how changes in water quality induced by an aquatic trophic cascade </span><span>affected foraging and growth of bumblebee colonies as well as foraging of solitary bees. While we expected fish predation to reduce top-down control of zooplankton on phytoplankton and thereby, indirectly, induce increased growth of toxic cyanobacteria</span><span>, we instead found the trophic cascade to induce the formation of algal surface mats that bumblebees used to access water under a severe heat wave and drought. This access to water was associated with higher bumblebee colony reproductive success, growth and weight compared to control colonies with no trophic cascade induced (and hence no algal surface mats). We also found marginal </span><span>but non-significant</span><span> effects on oilseed rape yield, but surprisingly with higher yields in the control treatment where bumblebees could not access water.</span><span>Our results provide new insights on how aquatic trophic cascades can lead to unpredicted ecological interactions across the aquatic-terrestrial interface facilitated by climate change. Our study highlights the importance of water for the fitness of terrestrial ecosystem service providers under altered environmental conditions.</span></p>
Fig.4 in Genetic Diversity Of (Brassica Napus L.) Spring Oilseed Rape
Fig.4. Analysis of Molecular Variance among cultivars and within cultivars
Fig. 2 in Commonly Found Species Of Ceutorhynchus (Coleoptera: Curculionidae) On The Oilseed Rape In Latvia
Fig. 2. Monitoring of adults of Ceutorhynchus, 2009.
Algal growth, bumblebee colony and individual development, bee behavior and yield of oilseed rape under a trophic cascade and extreme weather
Open the record for dataset details and reuse information.
Data from: Flower fields and pesticide use interactively shape pollen beetle infestation and parasitism in oilseed rape fields.
<p>MANUSCRIPT STILL UNDER REVISION</p> <ol> <li>Pollen beetles (Brassicogethes spp.) are the main pest of oilseed rape (OSR, Brassica napus) in Europe and responsible for massive yield losses. Upcoming pesticide resistances highlight the need for other means of crop protection, such as natural pest control. Sown flower fields aim to counteract the decrease of insect biodiversity in agricultural landscapes by providing breeding and foraging sites to ecosystem service providers such as parasitoids. However, the optimal age and size of flower fields to increase natural pest control is still unclear.</li> <li>We conducted experiments on 31 OSR fields located along a gradient of landscape-scale semi-natural habitat (SNH). OSR fields were located adjacent to flower fields which differed in age, continuity and size, or adjacent to crop fields or calcareous grasslands. In the OSR fields, pesticide free areas were established to examine interactive effects of pesticide use and flower field characteristics. The abundance of pollen beetle adults and larvae, parasitism and superparasitism rates in OSR were recorded at increasing distances to the adjacent fields.</li> <li>OSR next to flower fields maintained continuously for at least 6 years had the lowest numbers of pollen beetle larvae. Flower fields and calcareous grasslands increased pollen beetle parasitism in adjacent OSR fields compared to OSR fields neighbouring crop fields. However, the threshold for effective natural pest control of approximately 35% could only be reached in the pesticide free areas of OSR fields adjacent to calcareous grassland and continuous flower fields.</li> <li>In pesticide-sprayed areas, pollen beetle parasitism and superparasitism declined with increasing distance to the adjacent field, but they remained on the same level in areas without pesticides. Large flower fields (>1.5ha) increased parasitism and superparasitism more than small ones.</li> <li>Synthesis and applications: In general, older continuous flower fields decrease infestation with pollen beetle larvae and enhance parasitism rates in OSR. Furthermore, only flower fields larger than 1.5ha were able to push pollen beetle parasitism above the threshold level of 35%. Therefore, to promote natural pest control, it would be beneficial to maintain large flower fields for several years unmanaged, to create stable habitats for natural enemies. However, pesticide use has negative effects on OSR pollen beetle parasitism and can abrogate positive effects of flower fields on natural pest control. This study highlights that sown flower fields have the potential to increase natural pest control in OSR, but this potential is depending on its age and size and can be hindered by pesticide use.</li> </ol>
Data from: The relation between oilseed rape and pollination of later flowering plants varies across plant species and landscape contexts
Increasing cultivation of oilseed rape may have consequences for pollinators and wild plant pollination. By providing pollinating insects with pollen and nectar, oilseed rape benefits short-tongued, generalist insect species. Long-tongued bumble bee species, specialized to other flower types, may instead be negatively affected by increased competition from the generalists (e.g. due to nectar-robbing of long-tubed flowers) after oilseed rape has ceased flowering. We expected that the increased abundance of short-tongued pollinators and reduced abundance of long-tongued bumble bees in landscapes with a high proportion of oilseed rape would impact the pollination of later flowering wild plant species. In addition, we expected contrasting effects on plants pollinated by short-tongued pollinators and those pollinated by long-tongued bumble bees. We predicted that semi-natural grasslands, which provide insects with alternative floral resources, would reduce both negative and positive effects on pollination by mitigating competition between pollinators. In 16 semi-natural grasslands, surrounded by agricultural landscapes, with a variation in both the proportion of oilseed rape and the proportion of semi-natural grassland within 1 km, we studied reproductive output in two species of potted plants with different pollination strategies: the woodland strawberry (Fragaria vesca) and red clover (Trifolium pratense). The first species is mainly pollinated by short-tongued pollinators, e.g. hoverflies and solitary bees, and the latter by long-tongued bumble bees. Both species flowered after oilseed rape. Strawberry weight was higher in landscapes with a high proportion of oilseed rape, but only in landscapes with a low proportion of semi-natural grassland. The proportion of developed achenes was also positively related to the proportion of oilseed rape, but only during the latest flowering period. In contrast, red clover seed set was unrelated to the proportion of oilseed rape. Whereas the discrepancy between the two strawberry measurements calls for further research, this study suggests that oilseed rape can affect later flowering plants and that the impact differs among species.
Data from: Genetic diversity of oilseed rape fields and feral populations in the context of coexistence with GM crops
Despite growing concern about transgenes escaping from fields, few studies have analysed the genetic diversity of crops in an agroecosystem over several years. Accurate information about the dynamics and relationship of the genetic diversity of crops in an agroecosystem is essential for risk assessment and policies concerning the containment of genetically modified crops and their coexistence with crops grown by conventional practices. Here, we analysed the genetic diversity of oilseed rape plants from fields and feral populations over 4 years in an agricultural landscape of 41 km2. We used exact compatibility and maximum likelihood assignment methods to assign these plants to cultivars. Even pure lines and hybrid cultivar seed lots contained several genotypes. The cultivar diversity in fields reflected the conventional view of agroecosystems quite well: that is, there was a succession of cultivars, some grown for longer than others because of their good performance, some used for one year and then abandoned, and others gradually adopted. Three types of field emerged: fields sown with a single cultivar, fields sown with two cultivars, and unassigned fields (too many cultivars or unassigned plants to reliably assign the field). Field plant diversity was higher than expected, indicating the persistence of cultivars that were grown for only one year. The cultivar composition of feral populations was similar to that of field plants, with an increasing number of cultivars each year. By using genetic tools, we found a link between the cultivars of field plants in a particular year and the cultivars of feral population plants in the following year. Feral populations on road verges were more diverse than those on path verges. All of these findings are discussed in terms of their consequences in the context of coexistence with genetically modified crops.
Exploring multitrophic interactions in oilseed rape fields reveals the prevailing role of Carabidae
<p>In cropped fields, birds are often at the highest position in the food chain, feeding on pest arthropods and their intermediate predators in a process known as intraguild predation. The net effects of bird predation on phytophagous insect populations (feeding on plants) are difficult to predict without comprehensively describing prey-predator communities and their complex interplay. We sampled bird and arthropod communities in 30 oilseed rape fields in the spring of 2019 and 2020 in France. To assess the top-down control of arthropods by birds, we used a vertebrate exclusion experiment. Using a taxonomic and functional trait-based approach, we determined the direct and indirect influences of birds on arthropod predators and phytophagous insect populations in arable crops. We observed a negative relationship between the abundance of Carabidae and phytophagous insects but not with the other predator group suggesting the key role of Carabidae on phytophagous insects in agroecosystem. We found no statistical evidence of intraguild predation from birds towards intermediate predators. Despite the lack of overall effect of predator functional diversity on their prey, we highlighted the negative relationship between the functional complementarity (through functional evenness) of Carabidae and the abundance of phytophagous insects. This result suggests that functional complementarity between Carabidae species could help to reduce phytophagous insect populations. We analysed the effect of agricultural practices on these multitrophic interactions, showing that pesticide intensity only had detrimental effects on Carabidae abundance, while the frequency of tillage did not affect the studied communities. Complementary indices used to depict communities are helpful to better understand the mechanisms underlying trophic relationships.</p>
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